Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?
It does make a difference on polyacrylamide. A and C are faster while G and T are slower.
Image from publication:
The "standards" are AAA/TTT/GGG/CCC molecules.
Practically speaking I have never seen a difference, but the agarose gels usually used in the lab do not have the highest resolution. There is one paper showing that the form (A- or B- form) and the GC-content play a role since DNA molecules of higher GC content are less flexible and therefore have more problems getting through the agarose matrix. Interesting paper, but probably not very relevant in the lab (under "related publications" on the right side of the PubMed site you can find more on this topic):
There is however a technique, which makes use of the different GC content of DNA samples. It is called "Denaturing Gradient Gel Electrophoresis" and makes use of gradients (either chemical or temperature) to denaturate DNA on the gel. Depending on the GC content, this happens earlier or later, which influences the migration pattern (denaturated DNA is much bigger and slower). See here for more details.